Just this guys opinion, not the way I would rank them, but here are the 16 best 49er games.

NFC Conference Final ranked as 4th best 49ers game of all time

wrote:
4. The Validation (Jan 20, 2013): With Kaepernick replacing injured starter Alex Smith and playing well in his debut as an NFL starter in November, coach Jim Harbaugh made the controversial decision to stick with the second-year quarterback. When Kaepernick stayed cool and led San Francisco back from a 17-0 deficit at the Georgia Dome last Sunday, with the Niners prevailing 28-24 over the Falcons after a late defensive stand, Harbaugh’s decision was officially validated. And for the first time in 18 years, Niners fans are feeling Super.